Logic Pro 9 Heal separation + Flex


"Heal separation" in flex mode = Loosing your edits?

PT has a very cool command called "heal separation", and from what I can understand "merge regions per track" will also do this. If the cuts are "unnecessary" cuts, merging this region will not result in the creation of a new audio file, it will just "heal separation".
The problem is that if you do this with Flex on, apparently you loose your edits. I don't know for sure if it lost, but I'm positive the green and orange notes vanish.

This is kind of a big issue because, as the Flex tool creates random pops, and you must cut them off, how can I simply "heal separation" without loosing my Flex edits?